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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ), 'gf_id' => 'HOM05D001408', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001408' ), 'data_identifier' => 'HOM05D001408', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001408', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p25730' => 'bna', 'A04p16620' => 'bna', 'A05p20160' => 'bna', 'A08p33700' => 'bna', 'A09p57770' => 'bna', 'A09p64810' => 'bna', 'Aa31LG10G3850' => 'aar', 'Aa31LG1G3880' => 'aar', 'Aa31LG7G14590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1501' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2373' => 'aag', 'Actinidia00645' => 'ach', 'Actinidia05373' => 'ach', 'Actinidia08347' => 'ach', 'Actinidia20118' => 'ach', 'Actinidia26415' => 'ach', 'Actinidia31126' => 'ach', 'Actinidia40441' => 'ach', 'Ah.03g142710' => 'amhyb', 'Ah.09g226490' => 'amhyb', 'Ah.14g080940' => 'amhyb', 'Ah.15g094330' => 'amhyb', 'AL1G22000' => 'aly', 'AL1G58080' => 'aly', 'AL4G11430' => 'aly', 'Aqoxy6G00517' => 'aox', 'Aqoxy7G02017' => 'aox', 'Aqoxy7G02789' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8BB7J7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJU5BB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EK0RA6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KE22LN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LM66CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N0D15P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QNR6CS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S69VLQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U86EJZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY0I9M' => 'arhy', 'AT1G11020' => 'ath', 'AT1G50440' => 'ath', 'AT2G22120' => 'ath', 'ATR0171G028' => 'atr', 'ATR0564G421' => 'atr', 'ATR0626G025' => 'atr', 'ATR0716G078' => 'atr', 'Atru.chr1.2696' => 'acertr', 'Atru.chr4.325' => 'acertr', 'Atru.chr7.1245' => 'acertr', 'AUR62001344' => 'cqu', 'AUR62002045' => 'cqu', 'AUR62003750' => 'cqu', 'AUR62011065' => 'cqu', 'AUR62025660' => 'cqu', 'AUR62033442' => 'cqu', 'BcaB02g11147' => 'bca', 'BcaB08g35034' => 'bca', 'BcaC02g08741' => 'bca', 'BcaC05g27430' => 'bca', 'BcaC07g38634' => 'bca', 'BcaC07g41096' => 'bca', 'BolC4t26705H' => 'bol', 'BolC5t29672H' => 'bol', 'BolC5t29673H' => 'bol', 'BolC5t32117H' => 'bol', 'BolC8t49045H' => 'bol', 'BolC8t51663H' => 'bol', 'BolC8t52377H' => 'bol', 'BraA04t17296Z' => 'bra', 'BraA05t20925Z' => 'bra', 'BraA08t35286Z' => 'bra', 'BraA09t41169Z' => 'bra', 'BraA09t41814Z' => 'bra', 'C04p51120' => 'bna', 'C05p09320' => 'bna', 'C05p09330' => 'bna', 'C05p33840' => 'bna', 'C08p14070' => 'bna', 'C08p41000' => 'bna', 'C08p48380' => 'bna', 'CAN.G618.2' => 'can', 'CAN.G699.7' => 'can', 'CAN.G786.3' => 'can', 'CAN.G790.14' => 'can', 'CAN.G848.2' => 'can', 'CANSAT01G0518' => 'cansat', 'CANSAT01G1469' => 'cansat', 'CANSAT56G1866' => 'cansat', 'CARHR011220' => 'chi', 'CARHR040450' => 'chi', 'CARHR113240' => 'chi', 'Carub.0001s1059' => 'cru', 'Carub.0001s3951' => 'cru', 'Carub.0004s0125' => 'cru', 'Ca_00982_v3' => 'car', 'Ca_16552_v3' => 'car', 'Ca_21710_v3' => 'car', 'Cc04_g00210' => 'ccan', 'Cc06_g09030' => 'ccan', 'Cc07_g15750' => 'ccan', 'CDE02G3813' => 'cde', 'CDE05G0015' => 'cde', 'CDE05G3356' => 'cde', 'CDE06G2192' => 'cde', 'Cfa002149' => 'cfa', 'Cfa002726' => 'cfa', 'Cfa003326' => 'cfa', 'Cfa025614' => 'cfa', 'Ciclev10008976m.g' => 'ccl', 'Ciclev10026093m.g' => 'ccl', 'Ciclev10026281m.g' => 'ccl', 'CiPaw.01G090500' => 'cil', 'CiPaw.03G137200' => 'cil', 'CiPaw.03G239100' => 'cil', 'CiPaw.04G094600' => 'cil', 'ClCG01G019090' => 'cla', 'ClCG06G010750' => 'cla', 'ClCG07G014630' => 'cla', 'COL.COLO4_11042' => 'col', 'COL.COLO4_15585' => 'col', 'COL.COLO4_31172' => 'col', 'Cpa.g.c28217.2' => 'cpa', 'Cpa.g.c28217.3' => 'cpa', 'Cpa.g.sc155.20' => 'cpa', 'Cpa.g.sc334.3' => 'cpa', 'Cre12.g517800' => 'cre', 'Cre12.g517850' => 'cre', 'CsaV3_1G029630' => 'csa', 'CsaV3_3G030540' => 'csa', 'CsaV3_6G045770' => 'csa', 'CSS0001108' => 'camsi', 'CSS0020959' => 'camsi', 'CSS0030195' => 'camsi', 'CSS0030221' => 'camsi', 'CSS0048323' => 'camsi', 'DCAR_017846' => 'dca', 'DCAR_022612' => 'dca', 'DCAR_025283' => 'dca', 'Dinv19517' => 'din', 'Dinv20340' => 'din', 'Dinv21965' => 'din', 'Dinv36576' => 'din', 'Duzib150G0560' => 'dzi', 'Duzib187G0206' => 'dzi', 'Duzib187G1226' => 'dzi', 'Duzib187G1453' => 'dzi', 'Duzib192G0702' => 'dzi', 'Duzib235G1422' => 'dzi', 'Duzib264G0742' => 'dzi', 'ECA234G2636' => 'eca', 'ECA234G4639' => 'eca', 'ECA238G1866' => 'eca', 'EL10Ac6g15059' => 'bvu', 'EL10Ac7g18163' => 'bvu', 'EL10Ac8g18583' => 'bvu', 'Eucgr.C04161' => 'egr', 'Eucgr.F04027' => 'egr', 'Eucgr.I00344' => 'egr', 'FAN02G2669' => 'fan', 'FAN02G4345' => 'fan', 'FAN05G1663' => 'fan', 'FAN06G4179' => 'fan', 'FAN09G1717' => 'fan', 'FAN14G2979' => 'fan', 'FAN19G1030' => 'fan', 'FAN19G2584' => 'fan', 'FAN23G2290' => 'fan', 'FAN23G2869' => 'fan', 'FAN26G1158' => 'fan', 'FAN26G1351' => 'fan', 'FAN28G0235' => 'fan', 'FAN28G0849' => 'fan', 'FvH4_1g03950' => 'fve', 'FvH4_1g21840' => 'fve', 'FvH4_6g37040' => 'fve', 'FvH4_6g51470' => 'fve', 'Glyma.05G010700' => 'gma', 'Glyma.05G182200' => 'gma', 'Glyma.11G236400' => 'gma', 'Glyma.13G372600' => 'gma', 'Glyma.15G001100' => 'gma', 'Glyma.17G118400' => 'gma', 'Glyma.18G020800' => 'gma', 'Gohir.A05G019300' => 'ghi', 'Gohir.A06G118400' => 'ghi', 'Gohir.A11G197000' => 'ghi', 'Gohir.A13G198500' => 'ghi', 'Gohir.D01G084200' => 'ghi', 'Gohir.D01G093700' => 'ghi', 'Gohir.D02G146650' => 'ghi', 'Gohir.D05G020400' => 'ghi', 'Gohir.D06G096300' => 'ghi', 'Gohir.D06G122300' => 'ghi', 'Gohir.D06G127075' => 'ghi', 'Gohir.D06G146666' => 'ghi', 'Gohir.D08G042000' => 'ghi', 'Gohir.D08G093650' => 'ghi', 'Gohir.D10G155400' => 'ghi', 'Gohir.D11G225600' => 'ghi', 'Gohir.D12G053701' => 'ghi', 'Gohir.D12G123950' => 'ghi', 'Gohir.D13G203900' => 'ghi', 'Gorai.002G109900' => 'gra', 'Gorai.005G164200' => 'gra', 'Gorai.007G243100' => 'gra', 'Gorai.008G135000' => 'gra', 'Gorai.009G020600' => 'gra', 'Gorai.010G067100' => 'gra', 'Gorai.010G111000' => 'gra', 'Gorai.010G142500' => 'gra', 'Gorai.013G232700' => 'gra', 'GSVIVG01015477001' => 'vvi', 'GSVIVG01022196001' => 'vvi', 'GSVIVG01029539001' => 'vvi', 'HanXRQChr04g0094131' => 'han', 'HanXRQChr06g0179911' => 'han', 'HanXRQChr07g0197361' => 'han', 'HanXRQChr10g0316721' => 'han', 'HanXRQChr14g0445971' => 'han', 'Haze_16268' => 'cav', 'Haze_16273' => 'cav', 'Haze_25008' => 'cav', 'Haze_25636' => 'cav', 'Hma1.2p1_0018F.1_g012880' => 'hma', 'Hma1.2p1_0282F.1_g113390' => 'hma', 'Hma1.2p1_0308F.1_g120030' => 'hma', 'Hma1.2p1_0517F.1_g170760' => 'hma', 'Hma1.2p1_0517F.1_g170770' => 'hma', 'HPP92_014519' => 'vpl', 'HPP92_024083' => 'vpl', 'HPP92_027260' => 'vpl', 'Hund05676' => 'sun', 'Hund09161' => 'sun', 'Hund13652' => 'sun', 'Hund26463' => 'sun', 'Hund29633' => 'sun', 'Hund29635' => 'sun', 'Lalb_Chr08g0231271' => 'lal', 'Lalb_Chr11g0075211' => 'lal', 'Lalb_Chr13g0302121' => 'lal', 'Lalb_Chr14g0376191' => 'lal', 'Lj2A266G62' => 'lonja', 'Lj3g0017779' => 'lja', 'Lj4A879G63' => 'lonja', 'Lj4g0017489' => 'lja', 'Lj6g0024801' => 'lja', 'Lj7C636T1' => 'lonja', 'Lsat_1_v5_gn_1_1381' => 'lsa', 'Lsat_1_v5_gn_1_39440' => 'lsa', 'Lsat_1_v5_gn_2_67680' => 'lsa', 'Lsat_1_v5_gn_5_97600' => 'lsa', 'Lsat_1_v5_gn_8_58101' => 'lsa', 'Manes.06G050600' => 'mes', 'Manes.06G177100' => 'mes', 'Manes.12G139800' => 'mes', 'Manes.13G088500' => 'mes', 'Manes.14G007900' => 'mes', 'Manes.14G128500' => 'mes', 'Mapoly0033s0166' => 'mpo', 'Mapoly0061s0128' => 'mpo', 'MBI01_g34146_MAGBIO' => 'mbi', 'MBI01_g44858_MAGBIO' => 'mbi', 'MBI02_g34273_MAGBIO' => 'mbi', 'MBI04_g00946_MAGBIO' => 'mbi', 'MBI13_g34037_MAGBIO' => 'mbi', 'MD01G1021800' => 'mdo', 'MD02G1038000' => 'mdo', 'MD09G1164700' => 'mdo', 'MD15G1178300' => 'mdo', 'MD15G1330300' => 'mdo', 'MD17G1163500' => 'mdo', 'Medtr2g105850' => 'mtr', 'Medtr3g013530' => 'mtr', 'Medtr3g087920' => 'mtr', 'Medtr4g113520' => 'mtr', 'MELO3C007787.2' => 'cme', 'MELO3C026628.2' => 'cme', 'MELO3C030125.2' => 'cme', 'MELO3C030624.2' => 'cme', 'Migut.H02408' => 'egut', 'Migut.I01193' => 'egut', 'Migut.L00063' => 'egut', 'Migut.L00090' => 'egut', 'MSTRG.10880' => 'ama', 'MSTRG.15738' => 'ama', 'MSTRG.22502' => 'ama', 'MSTRG.2544' => 'ama', 'Nitab4.5_0000010g0070' => 'nta', 'Nitab4.5_0000818g0030' => 'nta', 'Nitab4.5_0004756g0050' => 'nta', 'Nitab4.5_0005096g0040' => 'nta', 'Nitab4.5_0005096g0050' => 'nta', 'Nitab4.5_0005664g0010' => 'nta', 'Nitab4.5_0005739g0040' => 'nta', 'Nitab4.5_0006788g0030' => 'nta', 'Nitab4.5_0006788g0040' => 'nta', 'Nitab4.5_0009562g0020' => 'nta', 'Nn1g05233' => 'nnu', 'Nn2g11918' => 'nnu', 'Nn8g39351' => 'nnu', 'Nn8g40790' => 'nnu', 'Oeu002189.1' => 'oeu', 'Oeu002191.1' => 'oeu', 'Oeu053756.2' => 'oeu', 'Oeu056483.2' => 'oeu', 'Oeu061153.1' => 'oeu', 'Oeu062491.1' => 'oeu', 'Os01g0610700' => 'osa', 'Os02g0132300' => 'osa', 'Os08g0384900' => 'osa', 'Os11g0604600' => 'osa', 'Peaxi162Scf00038g02531' => 'pax', 'Peaxi162Scf00204g00312' => 'pax', 'Peaxi162Scf00295g00016' => 'pax', 'Peaxi162Scf00295g00017' => 'pax', 'Peaxi162Scf00361g00079' => 'pax', 'Peaxi162Scf00440g00223' => 'pax', 'PGR004G2718' => 'pgr', 'PGR102G1464' => 'pgr', 'PGR102G1977' => 'pgr', 'PGSC0003DMG400006340' => 'stu', 'PGSC0003DMG400009191' => 'stu', 'PGSC0003DMG400012799' => 'stu', 'PGSC0003DMG400030103' => 'stu', 'PGSC0003DMG400030296' => 'stu', 'Phvul.001G249400' => 'pvu', 'Phvul.002G263200' => 'pvu', 'Phvul.003G160700' => 'pvu', 'Phvul.005G185000' => 'pvu', 'Potri.005G081500' => 'ptr', 'Potri.006G154800' => 'ptr', 'Potri.007G085900' => 'ptr', 'Potri.008G005800' => 'ptr', 'Potri.010G252900' => 'ptr', 'Potri.018G073400' => 'ptr', 'Pp3c2_2130' => 'ppa', 'Prupe.3G022100' => 'ppe', 'Prupe.6G177400' => 'ppe', 'Prupe.7G237300' => 'ppe', 'Psat0s13936g0040' => 'psa', 'Psat0s3462g0120' => 'psa', 'Psat3g051880' => 'psa', 'Psat5g087840' => 'psa', 'Psat5g307080' => 'psa', 'PSO063G1684' => 'pso', 'PSO170G1908' => 'pso', 'PSO170G5111' => 'pso', 'PSO210G4192' => 'pso', 'PSO242G0003' => 'pso', 'PSO447G0338' => 'pso', 'PSO541G2806' => 'pso', 'PSO675G1259' => 'pso', 'QL02p087153' => 'qlo', 'QL05p084007' => 'qlo', 'QL06p033197' => 'qlo', 'RcHm_v2.0_Chr2g0089431' => 'rch', 'RcHm_v2.0_Chr2g0115731' => 'rch', 'RcHm_v2.0_Chr2g0149591' => 'rch', 'RcHm_v2.0_Chr5g0010901' => 'rch', 'Rhsim01G0087200' => 'rsi', 'Rhsim01G0087500' => 'rsi', 'Rhsim10G0154900' => 'rsi', 'Rhsim12G0215100' => 'rsi', 'RhsimUnG0219400' => 'rsi', 'Sabra05G0066700' => 'sbr', 'Sabra06G0122700' => 'sbr', 'Sabra07G0071100' => 'sbr', 'Sabra08G0002900' => 'sbr', 'Sabra10G0196800' => 'sbr', 'Sabra18G0062200' => 'sbr', 'SalBow3G0549' => 'sbo', 'SalBow6G5270' => 'sbo', 'Sc02g0006220' => 'sci', 'Sc07g0000570' => 'sci', 'Sc15g0001030' => 'sci', 'Sc18g0000860' => 'sci', 'Sc18g0000870' => 'sci', 'Sc23g0004840' => 'sci', 'Sed0020439' => 'sed', 'Sed0021419' => 'sed', 'Sed0023760' => 'sed', 'Sed0024294' => 'sed', 'Sed0025199' => 'sed', 'SEGI_01935' => 'sgi', 'SEGI_03668' => 'sgi', 'SEGI_23077' => 'sgi', 'SEGI_31838' => 'sgi', 'SGA_v2.0_scaffold2G01313' => 'sas', 'SGA_v2.0_scaffold51G18733' => 'sas', 'SGA_v2.0_scaffold71G23991' => 'sas', 'SHI11656' => 'shi', 'SHI31112' => 'shi', 'SMO147G0383' => 'smo', 'SMO339G0069' => 'smo', 'SMO351G0436' => 'smo', 'SMO365G0040' => 'smo', 'Solyc03g123930.1' => 'sly', 'Solyc03g123950.4' => 'sly', 'Solyc04g011570.3' => 'sly', 'Solyc04g054330.3' => 'sly', 'Solyc05g051800.3' => 'sly', 'Sopen03g041670' => 'spe', 'Sopen04g005750' => 'spe', 'Sopen04g023940' => 'spe', 'Sopen05g030280' => 'spe', 'Sp1g09710' => 'spa', 'Sp1g37270' => 'spa', 'Sp4g01140' => 'spa', 'TAR280G0005' => 'tar', 'TAR376G0472' => 'tar', 'TAR383G0246' => 'tar', 'TAR625G0724' => 'tar', 'TAR626G1435' => 'tar', 'TAR628G0703' => 'tar', 'TAR636G0529' => 'tar', 'THA.LOC104800465' => 'tha', 'THA.LOC104804151' => 'tha', 'THA.LOC104807711' => 'tha', 'THA.LOC104809010' => 'tha', 'Thecc.01G109300' => 'tca', 'Thecc.06G059100' => 'tca', 'Thecc.09G119900' => 'tca', 'Thhalv10000252m.g' => 'esa', 'Thhalv10008262m.g' => 'esa', 'Thhalv10011737m.g' => 'esa', 'TPR.G20517' => 'tpr', 'TPR.G21053' => 'tpr', 'TPR.G29279' => 'tpr', 'TPR.G9085' => 'tpr', 'TWI12G0945' => 'twi', 'TWI32G1093' => 'twi', 'TWI74G1078' => 'twi', 'TWI77G0258' => 'twi', 'unitig_32.g11242' => 'ugi', 'unitig_736.g22346' => 'ugi', 'vmacro06185' => 'vma', 'vmacro12927' => 'vma', 'vmacro12928' => 'vma', 'vmacro20671' => 'vma', 'VMungo1080G0918' => 'vmu', 'VMungo1215G1412' => 'vmu', 'VMungo1383G2402' => 'vmu', 'Zm00001eb055230' => 'zma', 'Zm00001eb115010' => 'zma', 'Zm00001eb161850' => 'zma', 'Zm00001eb167260' => 'zma', 'Zm00001eb231340' => 'zma' ) $gf_id = 'HOM05D001408' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001408' ) $data_identifier = 'HOM05D001408' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 6, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 19, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb231340' $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